LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units           lj
atom_style      atomic

pair_style      lj/cut 2.5

read_data       data.rigid
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  81 atoms
  read_data CPU = 0.001 seconds

velocity        all create 100.0 4928459

# 1 chain of connected bodies

group           clump1 id <> 1 9
9 atoms in group clump1
group           clump2 id <> 9 18
10 atoms in group clump2
group           clump3 id <> 18 27
10 atoms in group clump3
group           clump4 id <> 27 36
10 atoms in group clump4
group           clump5 id <> 36 45
10 atoms in group clump5
group           clump6 id <> 45 54
10 atoms in group clump6
group           clump7 id <> 54 63
10 atoms in group clump7
group           clump8 id <> 63 72
10 atoms in group clump8
group           clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5                       clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

neigh_modify    exclude group clump1 clump1
neigh_modify    exclude group clump2 clump2
neigh_modify    exclude group clump3 clump3
neigh_modify    exclude group clump4 clump4
neigh_modify    exclude group clump5 clump5
neigh_modify    exclude group clump6 clump6
neigh_modify    exclude group clump7 clump7
neigh_modify    exclude group clump8 clump8
neigh_modify    exclude group clump9 clump9

thermo          100

#dump           1 all atom 50 dump.rigid.poems

#dump           2 all image 100 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    2 pad 5

#dump           3 all movie 100 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    3 pad 5

timestep        0.0001
thermo          50
run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix poems command:

@Article{Mukherjee08,
 author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
 title = {Substructured molecular dynamics using multibody dynamics algorithms},
 journal = {Intl.~J.~Non-linear Mechanics},
 year =    2008,
 volume =  43,
 pages =   {1045--1055}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045742 
     850    17821.483    711.53827            0    3681.7854    7.4384281 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19374            0    3681.3037    11.787982 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184716 
    1150    20849.582    206.01696            0    3680.9472  -0.86699115 
    1200    21815.003    45.317409            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064083 
    1300    20780.781    217.36511            0    3680.8286    6.0538606 
    1350    20558.971    254.36489            0    3680.8601   -3.6773868 
    1400     21485.03    99.812843            0    3680.6511   -16.185479 
    1450    21771.107    52.159652            0    3680.6775   -2.4756656 
    1500    21520.949    93.503872            0    3680.3286    2.1023574 
    1550    21351.419    121.68131            0    3680.2511    5.5159875 
    1600    20778.804    216.92191            0    3680.0559    15.089203 
    1650    21477.636    100.21877            0    3679.8247    -1.104524 
    1700    18501.329    596.48084            0    3680.0357   -15.679806 
    1750    18563.639    587.34841            0    3681.2882    33.532316 
    1800    19110.174    494.82524            0    3679.8543    18.024079 
    1850    21364.178    119.23767            0    3679.9339    2.5290075 
    1900    20146.588    322.15506            0    3679.9197    5.7317368 
    1950    20692.674    231.25288            0    3680.0319    4.2977982 
    2000    20943.904    189.11229            0    3679.7629   -22.643749 
    2050    19667.815    401.87016            0    3679.8394    3.6240972 
    2100    20280.109    299.81759            0    3679.8357    7.4803647 
    2150    19181.146    483.63975            0    3680.4974    22.634167 
    2200    21301.194    130.53171            0    3680.7308    4.7072523 
    2250     20484.79    266.99736            0    3681.1291   -8.6583002 
    2300    18648.002    573.09962            0       3681.1   -5.2548835 
    2350    21515.851    95.225745            0    3681.2009   -9.3875216 
    2400     21462.37    104.21272            0    3681.2744   -29.459857 
    2450    20108.034    330.94394            0    3682.2829     35.37058 
    2500    20771.818    220.42545            0    3682.3951   -12.318936 
    2550    20502.815    265.09577            0    3682.2316   -22.726822 
    2600    21462.006     105.2733            0    3682.2744   -10.180394 
    2650    21009.656    180.72738            0    3682.3367    4.9580828 
    2700    18680.012    569.37179            0    3682.7071    21.114114 
    2750     21256.19    139.42201            0    3682.1203   -7.4744399 
    2800    21552.267    90.071446            0    3682.1159   -6.2906304 
    2850    20879.958    202.00905            0    3682.0021   0.57990903 
    2900    19018.645    512.35214            0    3682.1262    13.883084 
    2950    19819.365    378.55747            0     3681.785   -0.7348943 
    3000    20269.229    303.35149            0    3681.5563    6.3088075 
    3050    19236.727    475.99457            0    3682.1158   -10.703575 
    3100     18391.55    616.96976            0    3682.2281     9.850079 
    3150    20258.563    305.82076            0     3682.248    7.1951283 
    3200    20716.384    229.15502            0    3681.8856    2.9042294 
    3250    18662.237     572.0784            0    3682.4512    9.2108597 
    3300    19162.278    488.60646            0    3682.3195    3.3306562 
    3350    21235.679    142.98279            0    3682.2626   0.29397483 
    3400    17677.053    736.09247            0    3682.2679     32.75269 
    3450    20852.392    206.65618            0    3682.0548   -4.8319056 
    3500    21182.918    151.46754            0    3681.9539   -5.6330382 
    3550     20589.85    250.40724            0     3682.049    12.582133 
    3600    20973.659    186.28043            0    3681.8903    10.935266 
    3650    17838.632    707.92145            0    3681.0268   -17.200926 
    3700    21538.002    92.744409            0    3682.4114  -0.72124229 
    3750    21390.294    117.90865            0    3682.9576   -7.8431786 
    3800    17921.046    696.50311            0     3683.344   -9.4641531 
    3850    20356.471    290.22624            0    3682.9715    2.4593463 
    3900    20374.077    287.10249            0     3682.782   -1.9519082 
    3950    20563.915    255.29993            0     3682.619    -6.124649 
    4000    20991.467    184.76183            0    3683.3397    1.8954961 
    4050    17805.623    716.24698            0    3683.8509   -20.454944 
    4100    19916.389    363.86301            0    3683.2611  -0.27912557 
    4150    19221.623    480.01232            0    3683.6161   -11.562492 
    4200     20526.82    261.78571            0    3682.9224   -3.9522917 
    4250    20922.813     196.1799            0    3683.3154   0.11947446 
    4300     19956.66    357.78133            0    3683.8914    19.156093 
    4350     19735.73    394.45981            0    3683.7482    14.865775 
    4400    21702.656    67.099805            0    3684.2092   -13.502538 
    4450    18163.055    656.97231            0    3684.1482   -0.6243111 
    4500    17477.718    771.25976            0    3684.2127   -0.4664004 
    4550    20676.507    238.19814            0    3684.2827   -19.444969 
    4600    17322.922    796.77058            0    3683.9242    27.003966 
    4650    11905.158    1704.9151            0    3689.1082    15.574169 
    4700    18689.079    569.80982            0    3684.6563    -14.67311 
    4750    19821.745    381.01914            0    3684.6433    5.0436795 
    4800    20621.335    247.96269            0    3684.8518   -16.407263 
    4850    21923.814    30.965964            0     3684.935   -13.418244 
    4900    18840.555    544.41538            0    3684.5079    11.005357 
    4950    15366.601    1124.2481            0    3685.3482    17.412375 
    5000    18274.314    639.01311            0     3684.732    5.3261109 
    5050    21173.687    155.83673            0    3684.7845    5.4056809 
    5100    21738.219     61.75201            0    3684.7885    -2.631945 
    5150    16597.949    918.84841            0    3685.1732   -10.124101 
    5200    20752.758    225.95919            0    3684.7522   -5.2441372 
    5250    17652.088     741.2645            0    3683.2793    2.0080739 
    5300    19907.523    366.53115            0    3684.4516    8.4266792 
    5350    20104.189    334.14522            0    3684.8433     17.21925 
    5400    21499.848    101.71631            0    3685.0243   -6.1103541 
    5450    21203.533    151.14574            0     3685.068   -5.9468503 
    5500    21076.513    172.45652            0    3685.2088    5.1418181 
    5550    20158.398    325.56609            0    3685.2992   -1.6486034 
    5600    20787.836    221.19563            0     3685.835    -10.66805 
    5650    19687.154    404.77204            0    3685.9644    -23.49128 
    5700    20419.311    282.58328            0    3685.8017  -0.52808211 
    5750    19738.522    395.95893            0    3685.7126    1.3889817 
    5800    18300.025    635.66905            0    3685.6732    23.490447 
    5850    20585.004    255.02032            0    3685.8543  -0.20699939 
    5900    20373.839    290.15881            0    3685.7987   -7.9712187 
    5950    18163.832    659.91192            0    3687.2173    5.4494586 
    6000    21049.247    177.43029            0    3685.6382    2.9138342 
    6050    21239.803    145.77613            0    3685.7433   -1.4927769 
    6100    20686.361    237.86454            0    3685.5913  -0.95516297 
    6150    20461.754    275.31546            0    3685.6079   -3.4166412 
    6200    19264.208    474.73017            0    3685.4316    11.750757 
    6250    21180.813    155.31746            0    3685.4529    2.8188219 
    6300    21047.543     177.4394            0    3685.3632    1.8641486 
    6350    20232.576    313.17716            0    3685.2731    2.8150209 
    6400    20185.616    321.33454            0    3685.6038   -3.8697311 
    6450    18969.632    523.95865            0    3685.5639    0.6725512 
    6500    17592.574    753.49959            0    3685.5952   -1.2557393 
    6550    21279.049    138.42524            0    3684.9335    -1.208945 
    6600    21408.457     116.4143            0    3684.4904   -1.5332953 
    6650    19758.218    391.17316            0    3684.2096    1.8511312 
    6700    20766.943    223.44631            0    3684.6036   -2.3672623 
    6750    20399.631    284.09914            0    3684.0377   -5.4089876 
    6800    21296.628    135.14662            0    3684.5847   -3.8442549 
    6850    20641.481     244.4451            0     3684.692    1.4020639 
    6900     20852.81    209.23009            0    3684.6984    1.8512104 
    6950    20940.555    194.66882            0    3684.7614    -6.554676 
    7000    19496.988    435.28199            0      3684.78   -15.120269 
    7050    19796.829    385.04227            0    3684.5138   -4.1068804 
    7100    19945.264    360.42431            0     3684.635   -4.0629042 
    7150    19431.123    446.12911            0    3684.6497   -6.8321751 
    7200    16864.851    873.80043            0    3684.6089    14.309069 
    7250     20438.75    277.85982            0    3684.3181    -11.41223 
    7300    17688.684    734.01576            0    3682.1298    35.938373 
    7350    21573.419     88.63421            0     3684.204   -3.9032749 
    7400    21198.486    150.72249            0    3683.8034   -7.1477117 
    7450    20586.708    252.93928            0    3684.0572   -7.6634645 
    7500    21815.377    48.180377            0    3684.0765   0.97457507 
    7550    17791.352    718.87564            0     3684.101    28.248235 
    7600    21828.874    45.928597            0    3684.0742  -0.25814944 
    7650    20827.961    212.35674            0    3683.6835   -3.4083384 
    7700    21319.176    130.43547            0    3683.6315   -12.434856 
    7750    20127.904    328.69643            0    3683.3471   -16.975711 
    7800    21741.772    59.679206            0    3683.3078    3.6261863 
    7850    19612.334    414.37418            0    3683.0964    1.3763274 
    7900    20071.318    337.74624            0    3682.9658  -0.40982763 
    7950    17925.664    695.29582            0    3682.9065    17.104439 
    8000    19125.978    492.76383            0    3680.4268    10.807662 
    8050    20233.848    310.42681            0    3682.7347    13.386237 
    8100    20551.619    257.86699            0    3683.1368    -13.97515 
    8150    21578.323     86.88362            0    3683.2708   -9.6811587 
    8200    21154.833    157.72897            0    3683.5344   0.62312375 
    8250    21321.143    129.83967            0    3683.3636    1.9536438 
    8300    21041.696    176.04177            0    3682.9911    4.7475567 
    8350     19883.39    369.32649            0    3683.2247   -7.0959328 
    8400    21626.067    79.062992            0    3683.4075   -14.919059 
    8450    21375.201    120.86836            0    3683.4019   -5.3461514 
    8500    20281.059    303.10304            0    3683.2796    3.7975093 
    8550    21170.533    154.48432            0    3682.9065   -1.1568561 
    8600    17754.931    724.00158            0    3683.1568     14.15254 
    8650    20685.478    235.65879            0    3683.2385   -5.2694179 
    8700    21489.165    101.90509            0    3683.4326   -4.2510612 
    8750    21106.682    165.41638            0    3683.1968   -3.9186708 
    8800    19149.516     491.5843            0    3683.1702   -11.419849 
    8850    21451.865     108.1814            0    3683.4923   -7.8256219 
    8900      19567.4    421.81206            0    3683.0454  -0.71997056 
    8950    20934.097    194.48033            0    3683.4965   -7.0106879 
    9000    18531.559    595.25957            0    3683.8528    3.7449399 
    9050    18868.821    537.22549            0     3682.029    9.9926092 
    9100    19972.527    354.73119            0    3683.4858  -0.30871263 
    9150    19641.651    409.18618            0    3682.7947   -1.3036238 
    9200     20019.08    346.19657            0    3682.7099    6.7425386 
    9250    19259.286    473.04973            0    3682.9308   -24.120659 
    9300    21597.757    82.971857            0     3682.598   -13.748483 
    9350    19348.379    457.23576            0    3681.9656    3.1571402 
    9400    19129.588    493.35235            0     3681.617    8.6293783 
    9450    20337.025    291.20959            0    3680.7138    6.8590795 
    9500    20581.788    249.65891            0    3679.9569   -18.892836 
    9550    19482.069     433.0077            0    3680.0192    23.029778 
    9600    19182.794    482.96871            0     3680.101   -11.081731 
    9650    20086.771     332.5311            0    3680.3263   -18.939681 
    9700    20274.046    300.98818            0    3679.9959    6.7538762 
    9750    18743.595    555.08045            0    3679.0129    8.2757138 
    9800    19464.311    435.66288            0    3679.7148    7.0528759 
    9850    21249.848    138.27382            0    3679.9152   -10.847402 
    9900    21156.214    153.84621            0    3679.8819   -7.8359674 
    9950    21643.134    72.547515            0    3679.7365   -10.507744 
   10000    19587.948    414.64942            0    3679.3075    6.1173553 
Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms

Performance: 36474.344 tau/day, 4221.568 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.005348   | 0.024925   | 0.056071   |  12.2 |  1.05
Neigh   | 0.0075012  | 0.022046   | 0.043933   |   9.3 |  0.93
Comm    | 0.13135    | 0.16461    | 0.1917     |   5.9 |  6.95
Output  | 0.0036298  | 0.004271   | 0.0056384  |   1.2 |  0.18
Modify  | 2.1147     | 2.1322     | 2.1418     |   0.7 | 90.01
Other   |            | 0.02072    |            |       |  0.87

Nlocal:          20.25 ave          81 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:             41 ave          78 max          11 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs:          193.5 ave         774 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 774
Ave neighs/atom = 9.5555556
Neighbor list builds = 989
Dangerous builds = 915
Total wall time: 0:00:02
